Kochi was a fishing village in the Kingdom of Kochi in the pre-colonial Kerala. The territory that would be later known as Fort Kochi was granted to the Portuguese in 1503 by the Rajah of Kochi, after the forces of Afonso de Albuquerque helped him fighting the forces of Saamoothiri of Kozhikode. The Rajah also gave them permission to build Fort Emmanuel near the waterfront to protect their commercial interests. The first part of the name Fort Kochi comes from this fort, which the Dutch later destroyed. The Portuguese built their settlement behind the fort, including a wooden church, which was rebuilt in 1516 as a permanent structure, today known as the St Francis Church. Fort Kochi remained in Portuguese possession for 160 years. In 1683 the Dutch captured the territory from the Portuguese, destroyed many Portuguese institutions, particularly Catholic including convents. The Dutch held Fort Kochi in their possession for 112 years until 1795, when the British took control by defeating the Dutch. Foreign control of Fort Kochi ended in 1947 with the Indian independence.

A mix of old houses built by the Portuguese, Dutch and British in these colonial periods line the streets of Fort Kochi. St Francis Church was built in 1503 by the Portuguese as a Catholic church. Vasco da Gama was once buried in this church which now falls under the Church of South India and is one of the national monuments. Santa Cruz Basilica, also built by the Portuguese in the 16th century, was later destroyed by the British and rebuilt near the end of 19th century. The landmark that causes more public and visitor interest is a series of precolonial Chinese fishing nets on the waterfront, believed to have been introduced by Chinese traders in the early 14th century.